1013-00005
· Genome Dx Therapeutics Inc · Pre-Filing
claim-chart-271-patent.xlsx
DOCUMENT
Litigation
[sheet: Cover]
| Field | Value |
| Document Title | Claim Chart: U.S. Patent No. 10,438,271 vs. Helios ProstaSignal™ Genomic Classifier |
| Matter | Genome Dx Therapeutics Inc. v. Helios Precision Diagnostics, Inc. |
| Case No. | 3:25-cv-01847-JWL |
| Court | U.S. District Court, Northern District of California |
| Patent-in-Suit | U.S. Patent No. 10,438,271 — 'Methods for Predicting Prostate Cancer Outcomes Using Multi-Gene Expression Classifiers' |
| Filing Date | June 14, 2016 |
| Issue Date | October 8, 2019 |
| Expiration Date | June 14, 2036 |
| Named Inventors | Dr. Rajan Mehta, Dr. Carolyn Xu, Dr. David Petrossian |
| Accused Product | ProstaSignal™ Genomic Classifier (Helios Precision Diagnostics, Inc.) |
| ProstaSignal™ Commercial Launch Date | October 7, 2024 |
| Claims Asserted | Claims 1, 3, 5, 7, 12, and 18 |
| Prepared By | Peter Vassiliev, Lead Associate, Calderwood & Harkness LLP |
| Reviewed By | Catherine Bloom, Responsible Partner, Calderwood & Harkness LLP |
| Prepared For | Genome Dx Therapeutics Inc. — ATTORNEY WORK PRODUCT / PRIVILEGED & CONFIDENTIAL |
| Date Prepared | March 2025 (updated February 2026) |
| Client Contact | Victoria Sung, General Counsel, GenomeDx; Dr. Kevin Ostrowski, VP intellectual Property, GenomeDx |
[sheet: Claim 1]
| Element No. | Claim Language | Claim Element Description | ProstaSignal™ Corresponding Feature | Evidence / Source | Infringement Theory | Notes |
| 1[preamble] | A method for prognosing the likelihood of clinical recurrence following radical prostatectomy comprising: | Preamble — method for prognosing clinical recurrence post-radical prostatectomy | ProstaSignal™ is marketed and performed as a prognostic test for prostate cancer patients following radical prostatectomy. Helios's product literature and MAAA code 0239M application describe the test as predicting likelihood of disease recurrence after surgery. ProstaSignal™ generates a 'ProstaScore' from 0 to 100 that is correlated with clinical recurrence risk. | Helios ProstaSignal™ product brochure (EV-001); Helios MAAA code 0239M application to MolDX, September 2024 (EV-006); Helios website (prostasignal.heliosprecision.com); Helios clinical validation publication(s) (EV-004); Deposition topics for Dr. Nathan Ashford (CEO) and Dr. Elaine Kossack (CSO) | Literal | Preamble is limiting to the extent it recites a specific clinical context (post-radical prostatectomy prognosis). ProstaSignal™ is expressly directed to this use case. |
| 1(a) | obtaining a biological sample containing tumor RNA; | Step (a) — obtaining biological sample containing tumor RNA | ProstaSignal™ test protocol requires submission of a formalin-fixed paraffin-embedded (FFPE) prostate tumor tissue specimen from which RNA is extracted. Helios's CLIA-certified laboratory at 9830 Mesa Rim Road, Suite 140, San Diego, CA 92121 receives FFPE tissue blocks or slides from pathology departments and extracts total RNA including tumor RNA for gene expression profiling. | Helios laboratory standard operating procedures (SOPs) for specimen receipt and RNA extraction (EV-003); Helios CLIA certification documents; ProstaSignal™ test requisition form (EV-007); Helios technical white paper on RNA extraction methodology | Literal | Biological sample containing tumor RNA is inherent in any gene-expression-based diagnostic test performed on prostate tumor tissue. |
| 1(b) | measuring expression levels of a panel of at least 22 genes selected from a predefined gene set; | Step (b) — measuring expression levels of ≥22 genes from predefined gene set | ProstaSignal™ measures expression levels of a panel of 24 genes. Of these 24 genes, 19 overlap with the predefined gene set recited in the '271 Patent specification (Table 1). The claim requires 'at least 22 genes selected from a predefined gene set' — ProstaSignal™'s 24-gene panel includes at least 19 genes from GenomeDx's predefined set plus 5 additional genes. The 24-gene panel satisfies the 'at least 22 genes' numerical threshold. The phrase 'selected from a predefined gene set' is construed to mean that the panel includes genes drawn from the gene set disclosed in the patent, not that all genes must come exclusively from that set. | Helios internal gene list for ProstaSignal™ (produced in discovery) (EV-002); GenomeDx comparison analysis of 19-of-24 gene overlap (EV-009); '271 Patent specification, Table 1 (predefined gene set) (EV-010); Expert analysis by Dr. Franklin Ogawa (proposed technical expert, Stanford) | Both | Key disputed element. Helios may argue that because only 19 of 24 genes overlap, the limitation is not met. GenomeDx's position: the claim requires 'at least 22 genes' total and that they be 'selected from a predefined gene set' — the 24 genes include at least 22 genes total, satisfying the numerical threshold, and 19 are drawn from the predefined set. Alternative DOE argument: if literal infringement is not found, the 19-gene overlap performs substantially the same function (prognostic classification) in substantially the same way (expression measurement) to achieve substantially the same result (risk stratification). Claim construction of 'predefined gene set' will be critical — see Preliminary Claim Construction Memorandum. |
| 1(c) | applying a trained machine-learning classifier to generate a risk score; | Step (c) — applying trained ML classifier to generate risk score | ProstaSignal™ applies a gradient-boosted decision tree (GBDT) classifier to the measured gene expression values to generate a numerical 'ProstaScore' ranging from 0 to 100. The '271 Patent claims recite a 'trained machine-learning classifier' without limiting the type of ML algorithm. Gradient-boosted decision trees are a well-recognized category of machine-learning classifiers. The ProstaScore is a 'risk score' within the plain meaning of the claim. | Helios algorithm documentation (produced under Highly Confidential — Attorneys' Eyes Only designation per Protective Order entered December 18, 2025) (EV-002); Helios clinical validation study data (EV-004); ProstaSignal™ technical specifications; Testimony of Dr. Anton Rykov (Senior Scientist, Bioinformatics, Helios) — anticipated deposition | Literal | GenomeDx's position: 'trained machine-learning classifier' is a broad term encompassing random forests, gradient-boosted trees, support vector machines, neural networks, and other supervised learning algorithms. GBDT is literally a trained machine-learning classifier. Helios may argue the specification limits 'classifier' to random forests; however, Claim 1 of the '271 Patent does not recite 'random-forest' — that limitation appears only in the '893 Patent. Prosecution history supports broad construction: applicant did not narrow the classifier type in Claim 1 during prosecution. |
| 1(d) | classifying the patient into a risk category based on the score. | Step (d) — classifying patient into risk category based on score | ProstaSignal™ classifies each patient into one of three risk categories — Low, Intermediate, or High — based on the generated ProstaScore value. Threshold cutoffs are applied to the 0–100 ProstaScore to assign the risk category, which is reported to the ordering healthcare provider. | ProstaSignal™ sample patient report (EV-005); Helios product literature describing Low / Intermediate / High risk stratification (EV-001); Helios clinical validation study defining ProstaScore cutoff thresholds (EV-004); Helios marketing materials and sales training documents | Literal | Direct mapping. ProstaSignal™ expressly classifies patients into named risk categories based on the computed score. |
[sheet: Claim 3]
| Element No. | Claim Language | Claim Element Description | ProstaSignal™ Corresponding Feature | Evidence / Source | Infringement Theory | Notes |
| 3[dependency] | The method of claim 1, | Claim 3 depends from Claim 1 — all elements of Claim 1 are incorporated by reference | All elements of Claim 1 are met by ProstaSignal™ as mapped in the Claim 1 tab. | See Claim 1 tab for all Claim 1 evidence | Literal | All Claim 1 elements are incorporated. See Claim 1 tab for full element-by-element mapping. |
| 3(a) | wherein the biological sample is a formalin-fixed paraffin-embedded (FFPE) tissue specimen. | Claim 3 adds: biological sample is FFPE tissue specimen | ProstaSignal™ is performed exclusively on FFPE prostate tumor tissue specimens. Helios's test requisition form and laboratory SOPs specify that the input sample must be an FFPE tissue block or unstained slides cut from FFPE blocks. This is the standard tissue preservation method used in pathology for post-surgical prostate specimens. | Helios test requisition form (EV-007); Helios laboratory SOPs (EV-003); ProstaSignal™ specimen requirements documentation; Helios CLIA laboratory protocols at 9830 Mesa Rim Road, San Diego, CA 92121 | Literal | Straightforward mapping. FFPE is the standard specimen type for post-prostatectomy genomic testing. No dispute anticipated on this limitation. |
[sheet: Claim 5]
| Element No. | Claim Language | Claim Element Description | ProstaSignal™ Corresponding Feature | Evidence / Source | Infringement Theory | Notes |
| 5[dependency] | The method of claim 1, | Claim 5 depends from Claim 1 — all elements of Claim 1 are incorporated by reference | All elements of Claim 1 are met by ProstaSignal™ as mapped in the Claim 1 tab. | See Claim 1 tab for all Claim 1 evidence | Literal | All Claim 1 elements are incorporated. See Claim 1 tab for full element-by-element mapping. |
| 5(a) | wherein measuring expression levels comprises performing quantitative reverse transcription polymerase chain reaction (RT-qPCR) or microarray-based expression profiling. | Claim 5 adds: expression measurement via RT-qPCR or microarray | ProstaSignal™ measures gene expression levels using a custom microarray-based expression profiling platform. Helios's technical documentation describes a proprietary microarray chip designed to capture expression data for the 24-gene panel plus reference genes. This falls within the 'microarray-based expression profiling' alternative recited in Claim 5. | Helios technical white paper on ProstaSignal™ platform; Helios algorithm documentation (EV-002); Helios microarray chip specifications (produced in discovery under AEO designation); anticipated testimony of Dr. Elaine Kossack and Dr. Anton Rykov | Literal | Claim 5 is written in the alternative (RT-qPCR or microarray). ProstaSignal™ meets the microarray alternative. No dispute anticipated on this limitation. |
[sheet: Claim 7]
| Element No. | Claim Language | Claim Element Description | ProstaSignal™ Corresponding Feature | Evidence / Source | Infringement Theory | Notes |
| 7[dependency] | The method of claim 1, | Claim 7 depends from Claim 1 — all elements of Claim 1 are incorporated by reference | All elements of Claim 1 are met by ProstaSignal™ as mapped in the Claim 1 tab. | See Claim 1 tab for all Claim 1 evidence | Literal | All Claim 1 elements are incorporated. See Claim 1 tab for full element-by-element mapping. |
| 7(a) | wherein the trained machine-learning classifier is trained on a cohort of patient samples comprising at least 200 patients with known clinical outcomes. | Claim 7 adds: classifier trained on cohort of ≥200 patients with known clinical outcomes | Helios's algorithm documentation and clinical validation publications indicate that the ProstaSignal™ gradient-boosted decision tree classifier was trained on a retrospective cohort of approximately 1,200 prostate cancer patient samples with known 5-year and 10-year clinical outcome data (metastasis, biochemical recurrence, cancer-specific mortality). This training cohort of ~1,200 patients far exceeds the 'at least 200 patients' threshold recited in Claim 7. | Helios clinical validation study manuscript(s) (EV-004); Helios algorithm training data documentation (EV-002, produced under AEO); anticipated deposition testimony of Dr. Elaine Kossack and Dr. Anton Rykov regarding training cohort composition and size | Literal | The training cohort size (~1,200) substantially exceeds the claimed minimum (200). No dispute anticipated on this limitation. |
[sheet: Claim 12]
| Element No. | Claim Language | Claim Element Description | ProstaSignal™ Corresponding Feature | Evidence / Source | Infringement Theory | Notes |
| 12[dependency] | The method of claim 1, | Claim 12 depends from Claim 1 — all elements of Claim 1 are incorporated by reference | All elements of Claim 1 are met by ProstaSignal™ as mapped in the Claim 1 tab. | See Claim 1 tab for all Claim 1 evidence | Literal | All Claim 1 elements are incorporated. See Claim 1 tab for full element-by-element mapping. |
| 12(a) | wherein the risk score is correlated with metastasis risk within a defined post-surgical time period. | Claim 12 adds: risk score correlated with metastasis risk within defined post-surgical time period | ProstaSignal™'s ProstaScore (0–100) is expressly designed and clinically validated as correlating with the risk of metastatic progression within 5 years following radical prostatectomy. Helios's clinical validation study reports hazard ratios and area-under-the-curve (AUC) statistics demonstrating the ProstaScore's correlation with 5-year metastasis-free survival. The 5-year post-surgical window constitutes a 'defined post-surgical time period.' | Helios clinical validation study (EV-004); ProstaSignal™ product literature and sample reports showing 5-year metastasis risk correlation (EV-001, EV-005); Helios MAAA code 0239M application describing intended clinical use (EV-006); anticipated expert testimony from Dr. Franklin Ogawa | Literal | ProstaSignal™ is explicitly designed for metastasis risk prediction within a defined time horizon. No dispute anticipated on this limitation. |